Name: RenLab-HiC-cortex Rep1

Organism: Mus musculus

Source: Mouse cortex

RE: HindIII

Sample ID: GSM938750

Mapping Statistics

File SRR501772 SRR501773 SRR501774 SRR501775 SRR501776
Total reads 26,241,072 26,688,189 26,459,526 26,116,841 44,209,842
First pair aligned 23,127,474 (88.13%) 23,730,961 (88.92%) 23,694,677 (89.55%) 23,365,054 (89.46%) 39,259,625 (88.80%)
Second pair aligned 21,294,849 (81.15%) 23,216,385 (86.99%) 23,333,789 (88.19%) 23,025,870 (88.16%) 38,254,961 (86.53%)
PCR duplicate paired reads 485,508 (1.85%) 549,837 (2.06%) 558,827 (2.11%) 547,749 (2.10%) 1,211,382 (2.74%)
Chimeric paired reads 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
Valid chimeric paired reads 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
Total mapped/paired reads 13,799,798 (52.59%) 15,070,879 (56.47%) 15,132,080 (57.19%) 14,917,919 (57.12%) 24,805,952 (56.11%)
Valid mapped/paired reads 13,314,290 (50.74%) 14,521,042 (54.41%) 14,573,253 (55.08%) 14,370,170 (55.02%) 23,594,570 (53.37%)

File SRR501777
Total reads 85,145,369
First pair aligned 75,767,102 (88.99%)
Second pair aligned 73,952,985 (86.85%)
PCR duplicate paired reads 3,663,545 (4.30%)
Chimeric paired reads 0 (0.00%)
Valid chimeric paired reads 0 (0.00%)
Total mapped/paired reads 47,986,086 (56.36%)
Valid mapped/paired reads 44,322,541 (52.06%)

HiC Read Statistics

Total reads 124,695,866
Chromosome not in fends 0 (0.00%)
PCR duplicates 0 (0.00%)
Outide RE cutsite range 2,674,136 (2.14%)
Insert larger than cutoff 53,890,465 (43.22%)
Fragment circularization 1,400,963 (1.12%)
Possible failed RE digest 13,506,627 (10.83%)
Valid cis reads 17,380,982 (13.94%)
Valid trans reads 35,842,693 (28.74%)
Unique cis fend pairs 14,550,358
Unique trans fend pairs 32,360,001

Insert Size Distribution

Fend Intra-chromosomal Interaction Distribution

Fend Inter-chromosomal Interaction Distribution

Best insert size

586